How to fix boolean cut failures?
To repair this kind of damage I would select all and press X (Delete) to start from scratch. 

Very similar result you can get easier without booleans and with clean topology by shrinkwraped edges over your terrain.


Add plane, slice it by Ctrl+R with value of desired amounth of cuts
Select one short edge, search for Select Similar > Lenght and delete them (X)
Subdivide all long edges in amount of desired detail
Rotate in desired angle of Z axis
Add Shrink Wrap modifier with Projection type, Target your terrain, Z axis, Positive, Apply
Select all vertices, Extrude (E) in Z axis, move below terrain level, Scale in Z to 0
Add Solidify modifier to get thickness


Simplified sketch of proces


Hires model (1000 slices)